Still it would be nice to have some sort of reasoning as to why they went for Armada.

Actually the name Armada does make sense in a manner of speaking. If you think about it, the central concept behind Armada, in fact it would be fair to roughly translate the Japanese name for Armada as "Legend of the Minicons.

Now granted, if you're approaching it from the concept of amassing a huge and powerful army (relatively speaking), then "Legion" would probably have been the more ideal choice (ie whoever possesses all the Minicons has a legion of them). However as the Minicons do transform into vehicles, you could loosely get away with using "Armada" instead.